Shake roofs have been around for centuries and are one of the original roofing materials. One issue with shake roofs that were installed in the last 30 years is the installation itself. Lath installation is no longer used and they are now installed upon decking with an underlining, or what we call roof felt.
The felt does make for a great water barrier, but because of improper spacing between the felt and the shakes, the shakes often cannot breathe or dry properly. Thus the shakes retain moisture, allowing for infestations to move in.
Over time, the shakes lose their integrity, which can lead to interior water damage and premature roof replacement if there is no regular roof maintenance or cleaning.
Many shake roof homeowners were never told they need to maintain their roof to reach the potential natural life span of anywhere from 40 to 60 years. Normally after a 10-year period of not cleaning, a homeowner will notice the green moss or mold, the lichen or the dark brown to black coloration of fungi.
At this point, many homeowners believe that a new roof is needed, when in reality, regular maintenance to remove and replace the deficient shakes and a good cleaning will keep damage from occurring and will allow the shakes to breathe and stay dry.
In regards to staining and sealing a shake roof, staining is fine for curb appeal but adds no real value to preserving the roof itself. Sealing a shake roof should never be done as this will keep the shakes from getting the air they need to stay dry.
In addition to cleaning you should make sure there is no debris left in the valleys and no trees hanging over the roof as this will cause moisture and shade. Also, it is a good idea to replace missing shakes, checked (cracked) and loose or missing ridge cap that does or will expose the inter-ply felt, as UV light can cause felt deterioration.
The best way to prevent leak damage is to maintain the roof on a regular basis and if you have a leak, call a professional roofer.